➔ Poster
AuthorsYannick Cogne 1, Christine Almunia 1, Olivier Pible 1, Duarte Gouveia 2, Arnaud Chaumot 2, Olivier Geffard 2, Jean Armengaud 1*
1 :
Innovative technologies for Detection and Diagnostics (Li2D), CEA Marcoule, BP17171, F-30207 BAGNOLS-SUR-CEZE - France
2 :
Milieux aquatiques, écologie et pollutions (UR MALY), CEMAGREF, 5 rue de la Doua, CS70077, 69626 Villeurbanne Cedex, France - France
* : Corresponding author
Abstract
Defining molecular markers to assess health status or modes of action of chemical contaminants in any sentinel organism is an important objective in ecotoxicology. With the long-term goal of testing the biological quality of freshwater systems, we developed a biomonitoring approach based upon a widespread sentinel organism, namely the crustacean amphipod
Gammarus fossarum. Biomarkers of interest from this organism, which are proteins whose abundance varies depending on the presence of pollutants, can be monitored by proteomics.
G. fossarum is a so-called "non-model" species because there is no reference genomic sequence for this genus. A reference protein sequence database can be obtained by
de novo assembly of mature transcript sequences with the help of proteogenomics data. To take into account the diversity of
Gammarus populations and cryptic species, a combination of bioinformatics tools for assembling RNAseq data and proteomic assignment is required. We choose the Galaxy working environment with an easy portable solution using Docker, a container management program runable under Windows. Galaxy Docker (developed by Björn Grüning) with one container per tool option provides version management as well as a high reproducibility of environment variables. The implementation for evaluating strategies for exploring molecular diversity through proteogenomics, including the management of data from new RNA sequencing technologies and their assembly will be detailed.
